Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: YVQJ2

Calculation Name: 3VUQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VUQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLX6

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1860212.106635
FMO2-HF: Nuclear repulsion 1788432.190177
FMO2-HF: Total energy -71779.916458
FMO2-MP2: Total energy -71991.470529


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:8:ALA)


Summations of interaction energy for fragment #1(A:8:ALA)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-3.318-1.794-0.022-0.614-0.8870.001
Interaction energy analysis for fragmet #1(A:8:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.003
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A10VAL00.0200.0023.7930.5621.959-0.021-0.603-0.7720.001
4A11LYS10.9880.9816.2960.7370.7370.0000.0000.0000.000
5A12ASP-1-0.881-0.9456.6680.3170.3170.0000.0000.0000.000
6A13LYS10.9850.9964.407-4.712-4.585-0.001-0.011-0.1150.000
7A14LYS10.9700.9859.278-0.078-0.0780.0000.0000.0000.000
8A15ARG10.9871.00111.568-0.258-0.2580.0000.0000.0000.000
9A16ALA00.0400.02812.414-0.033-0.0330.0000.0000.0000.000
10A17ILE00.0010.00012.085-0.052-0.0520.0000.0000.0000.000
11A18LEU0-0.0260.00715.182-0.036-0.0360.0000.0000.0000.000
12A19GLU-1-0.909-0.96117.2120.1870.1870.0000.0000.0000.000
13A20ALA00.0010.00317.880-0.022-0.0220.0000.0000.0000.000
14A21THR0-0.041-0.04718.922-0.024-0.0240.0000.0000.0000.000
15A22LEU00.0090.00921.280-0.019-0.0190.0000.0000.0000.000
16A23ALA00.0050.00822.698-0.015-0.0150.0000.0000.0000.000
17A24VAL00.003-0.00222.856-0.012-0.0120.0000.0000.0000.000
18A25LEU0-0.0070.03225.177-0.015-0.0150.0000.0000.0000.000
19A26ARG10.9060.96627.199-0.102-0.1020.0000.0000.0000.000
20A27GLH0-0.070-0.08026.726-0.007-0.0070.0000.0000.0000.000
21A28ARG10.8250.89327.799-0.165-0.1650.0000.0000.0000.000
22A29GLY00.0470.02930.440-0.007-0.0070.0000.0000.0000.000
23A30LEU00.007-0.03128.2560.0100.0100.0000.0000.0000.000
24A31SER00.0030.00329.7660.0040.0040.0000.0000.0000.000
25A32GLY00.0020.01030.7040.0010.0010.0000.0000.0000.000
26A33LEU0-0.0090.00523.3500.0160.0160.0000.0000.0000.000
27A34LYS10.9600.97525.290-0.161-0.1610.0000.0000.0000.000
28A35MET00.0450.02118.9990.0040.0040.0000.0000.0000.000
29A36GLU-1-0.868-0.90120.0440.2740.2740.0000.0000.0000.000
30A37GLU-1-0.731-0.81820.8300.2300.2300.0000.0000.0000.000
31A38VAL00.0000.00817.7030.0180.0180.0000.0000.0000.000
32A39ALA0-0.012-0.01916.2630.0340.0340.0000.0000.0000.000
33A40ARG10.8940.93916.203-0.215-0.2150.0000.0000.0000.000
34A41ARG10.8530.92217.908-0.210-0.2100.0000.0000.0000.000
35A42ALA0-0.016-0.00314.0850.0020.0020.0000.0000.0000.000
36A43GLU-1-0.953-0.95212.9780.8360.8360.0000.0000.0000.000
37A44VAL0-0.050-0.02210.4970.2310.2310.0000.0000.0000.000
38A45GLY00.0600.02912.331-0.140-0.1400.0000.0000.0000.000
39A46LYS11.0040.96914.224-0.282-0.2820.0000.0000.0000.000
40A47GLY0-0.019-0.01615.541-0.031-0.0310.0000.0000.0000.000
41A48THR00.0300.0149.5800.0000.0000.0000.0000.0000.000
42A49ILE00.0550.02811.835-0.021-0.0210.0000.0000.0000.000
43A50TYR0-0.083-0.02214.045-0.043-0.0430.0000.0000.0000.000
44A51LEU0-0.030-0.0029.782-0.025-0.0250.0000.0000.0000.000
45A52TYR0-0.109-0.0486.553-0.045-0.0450.0000.0000.0000.000
46A53PHE00.0180.00312.527-0.058-0.0580.0000.0000.0000.000
47A54ARG10.9921.01116.320-0.040-0.0400.0000.0000.0000.000
48A55ASP-1-0.837-0.95618.9340.1130.1130.0000.0000.0000.000
49A56LYS10.8950.92020.479-0.165-0.1650.0000.0000.0000.000
50A57ARG10.9530.98422.311-0.060-0.0600.0000.0000.0000.000
51A58ASP-1-0.839-0.92019.2250.0590.0590.0000.0000.0000.000
52A59LEU0-0.024-0.01317.209-0.007-0.0070.0000.0000.0000.000
53A60LEU0-0.039-0.02920.044-0.003-0.0030.0000.0000.0000.000
54A61LYS10.9210.96823.125-0.026-0.0260.0000.0000.0000.000
55A62ALA00.0310.01518.879-0.011-0.0110.0000.0000.0000.000
56A63LEU00.0000.00320.965-0.008-0.0080.0000.0000.0000.000
57A64VAL0-0.008-0.00322.021-0.008-0.0080.0000.0000.0000.000
58A65GLU-1-0.896-0.94723.213-0.001-0.0010.0000.0000.0000.000
59A66GLU-1-0.936-0.96618.4270.0200.0200.0000.0000.0000.000
60A67ARG10.8230.89922.760-0.072-0.0720.0000.0000.0000.000
61A68THR00.012-0.01925.515-0.005-0.0050.0000.0000.0000.000
62A69TRP0-0.017-0.00222.695-0.005-0.0050.0000.0000.0000.000
63A70ALA0-0.021-0.01824.623-0.008-0.0080.0000.0000.0000.000
64A71PHE00.0570.03426.343-0.004-0.0040.0000.0000.0000.000
65A72TYR0-0.029-0.04129.663-0.001-0.0010.0000.0000.0000.000
66A73ARG10.9611.00123.4170.0410.0410.0000.0000.0000.000
67A74GLU-1-0.960-0.98128.8390.0160.0160.0000.0000.0000.000
68A75VAL0-0.022-0.01231.107-0.002-0.0020.0000.0000.0000.000
69A76GLU-1-0.926-0.96530.553-0.046-0.0460.0000.0000.0000.000
70A77GLU-1-0.834-0.88731.306-0.018-0.0180.0000.0000.0000.000
71A78VAL0-0.010-0.00333.3250.0000.0000.0000.0000.0000.000
72A79VAL0-0.047-0.03436.5570.0000.0000.0000.0000.0000.000
73A80ARG10.7800.87032.7660.0390.0390.0000.0000.0000.000
74A81ARG10.7760.89334.2150.0060.0060.0000.0000.0000.000
75A82LYS10.9490.98238.1770.0260.0260.0000.0000.0000.000
76A83ALA00.019-0.00341.1740.0010.0010.0000.0000.0000.000
77A84PRO00.0550.02543.306-0.001-0.0010.0000.0000.0000.000
78A85PHE00.0770.04345.3210.0010.0010.0000.0000.0000.000
79A86PHE00.017-0.02145.7680.0010.0010.0000.0000.0000.000
80A87VAL00.0210.03742.8680.0020.0020.0000.0000.0000.000
81A88ARG10.8710.92440.6090.0190.0190.0000.0000.0000.000
82A89LEU0-0.030-0.01541.7030.0010.0010.0000.0000.0000.000
83A90GLU-1-0.864-0.94143.4240.0090.0090.0000.0000.0000.000
84A91GLU-1-0.936-0.98439.1260.0010.0010.0000.0000.0000.000
85A92VAL0-0.018-0.01738.3960.0030.0030.0000.0000.0000.000
86A93LEU00.004-0.00339.3740.0030.0030.0000.0000.0000.000
87A94ARG10.8920.93139.847-0.014-0.0140.0000.0000.0000.000
88A95ARG10.9560.97233.917-0.004-0.0040.0000.0000.0000.000
89A96ARG10.9290.98136.557-0.007-0.0070.0000.0000.0000.000
90A97LEU00.0130.00938.3730.0030.0030.0000.0000.0000.000
91A98ALA00.0210.01636.0590.0030.0030.0000.0000.0000.000
92A99TRP00.012-0.00329.4470.0050.0050.0000.0000.0000.000
93A100VAL0-0.031-0.01435.2970.0040.0040.0000.0000.0000.000
94A101GLN00.0260.01837.8350.0030.0030.0000.0000.0000.000
95A102GLU-1-0.781-0.84129.9840.0630.0630.0000.0000.0000.000
96A103TRP0-0.035-0.02930.8460.0060.0060.0000.0000.0000.000
97A104ARG10.8790.92834.525-0.027-0.0270.0000.0000.0000.000
98A105GLY00.0000.01336.1010.0010.0010.0000.0000.0000.000
99A106LEU0-0.047-0.02028.3840.0070.0070.0000.0000.0000.000
100A107TRP00.032-0.03625.5210.0050.0050.0000.0000.0000.000
101A108ALA00.0170.03631.224-0.002-0.0020.0000.0000.0000.000
102A109ALA0-0.017-0.01633.117-0.001-0.0010.0000.0000.0000.000
103A110VAL00.0180.00226.7480.0020.0020.0000.0000.0000.000
104A111ALA00.0130.00529.1070.0010.0010.0000.0000.0000.000
105A112ARG10.9110.95630.427-0.053-0.0530.0000.0000.0000.000
106A113GLU-1-0.916-0.95829.5500.0740.0740.0000.0000.0000.000
107A114ALA0-0.082-0.03925.8980.0020.0020.0000.0000.0000.000
108A115MET0-0.115-0.05127.255-0.006-0.0060.0000.0000.0000.000
109A116ASP-1-0.897-0.94129.6110.0340.0340.0000.0000.0000.000
110A117ASP-1-0.875-0.94132.1740.0070.0070.0000.0000.0000.000
111A118PRO0-0.016-0.01332.226-0.004-0.0040.0000.0000.0000.000
112A119THR00.0380.01433.373-0.002-0.0020.0000.0000.0000.000
113A120PRO0-0.008-0.02134.067-0.002-0.0020.0000.0000.0000.000
114A121TRP00.0730.03728.0880.0000.0000.0000.0000.0000.000
115A122LEU0-0.003-0.01132.978-0.002-0.0020.0000.0000.0000.000
116A123LYS10.9290.98235.1290.0000.0000.0000.0000.0000.000
117A124GLY00.0690.04634.586-0.002-0.0020.0000.0000.0000.000
118A125LEU0-0.029-0.01530.524-0.003-0.0030.0000.0000.0000.000
119A126HIS0-0.0020.00134.4930.0000.0000.0000.0000.0000.000
120A127GLU-1-0.943-0.98437.596-0.016-0.0160.0000.0000.0000.000
121A128HIS0-0.059-0.03531.911-0.004-0.0040.0000.0000.0000.000
122A129TYR00.0040.00036.174-0.001-0.0010.0000.0000.0000.000
123A130LEU00.0130.01537.715-0.001-0.0010.0000.0000.0000.000
124A131ARG10.9750.98434.7500.0250.0250.0000.0000.0000.000
125A132LEU00.0070.02234.110-0.001-0.0010.0000.0000.0000.000
126A133LEU00.0380.01638.6260.0000.0000.0000.0000.0000.000
127A134GLU-1-0.901-0.96242.018-0.018-0.0180.0000.0000.0000.000
128A135GLU-1-0.872-0.90737.851-0.033-0.0330.0000.0000.0000.000
129A136LEU00.0030.00541.546-0.001-0.0010.0000.0000.0000.000
130A137LEU0-0.014-0.02442.9520.0000.0000.0000.0000.0000.000
131A138ARG10.9080.95642.5290.0230.0230.0000.0000.0000.000
132A139SER00.0080.03543.6310.0000.0000.0000.0000.0000.000
133A140GLY00.0770.02745.7770.0000.0000.0000.0000.0000.000
134A141GLN0-0.092-0.04648.475-0.001-0.0010.0000.0000.0000.000
135A142SER0-0.101-0.04947.9040.0000.0000.0000.0000.0000.000
136A143GLU-1-0.905-0.97046.140-0.017-0.0170.0000.0000.0000.000
137A144GLY0-0.0160.01050.6020.0010.0010.0000.0000.0000.000
138A145ALA0-0.063-0.02650.4630.0010.0010.0000.0000.0000.000
139A146VAL0-0.019-0.00749.4160.0020.0020.0000.0000.0000.000
140A147ARG10.9990.99152.7300.0040.0040.0000.0000.0000.000
141A148THR00.0640.01554.0680.0000.0000.0000.0000.0000.000
142A149GLY0-0.0050.00554.9450.0000.0000.0000.0000.0000.000
143A150LEU0-0.040-0.00352.9530.0000.0000.0000.0000.0000.000
144A151SER00.0560.03251.288-0.001-0.0010.0000.0000.0000.000
145A152PRO00.0460.01446.9860.0010.0010.0000.0000.0000.000
146A153ARG10.9891.00242.8960.0140.0140.0000.0000.0000.000
147A154ALA0-0.022-0.01347.5070.0010.0010.0000.0000.0000.000
148A155THR00.028-0.00949.6290.0020.0020.0000.0000.0000.000
149A156ALA00.0140.01344.2130.0010.0010.0000.0000.0000.000
150A157ALA0-0.030-0.02345.6280.0020.0020.0000.0000.0000.000
151A158VAL0-0.0020.00546.9010.0020.0020.0000.0000.0000.000
152A159ILE00.0220.00544.7950.0020.0020.0000.0000.0000.000
153A160ALA0-0.046-0.03642.8340.0020.0020.0000.0000.0000.000
154A161ALA0-0.041-0.01043.8290.0020.0020.0000.0000.0000.000
155A162MET0-0.0280.01244.2720.0020.0020.0000.0000.0000.000
156A163GLY00.0330.00242.9390.0000.0000.0000.0000.0000.000
157A164CYS0-0.065-0.04043.3630.0020.0020.0000.0000.0000.000
158A165THR0-0.003-0.00345.9360.0000.0000.0000.0000.0000.000
159A166PRO00.0190.02246.4910.0000.0000.0000.0000.0000.000
160A167SER0-0.0040.03347.5110.0000.0000.0000.0000.0000.000
161A168LEU0-0.012-0.04949.1400.0000.0000.0000.0000.0000.000
162A169GLU-1-0.892-0.94643.8400.0300.0300.0000.0000.0000.000
163A170VAL0-0.066-0.03445.6290.0000.0000.0000.0000.0000.000
164A171GLU-1-0.795-0.86544.8390.0180.0180.0000.0000.0000.000
165A172ALA00.0620.02847.717-0.001-0.0010.0000.0000.0000.000
166A173TYR0-0.041-0.02547.557-0.002-0.0020.0000.0000.0000.000
167A174LEU00.010-0.00844.292-0.001-0.0010.0000.0000.0000.000
168A175GLU-1-0.880-0.94048.5240.0110.0110.0000.0000.0000.000
169A176HIS00.0130.00651.297-0.002-0.0020.0000.0000.0000.000
170A177LEU0-0.0180.00347.324-0.001-0.0010.0000.0000.0000.000
171A178MET0-0.030-0.01747.960-0.002-0.0020.0000.0000.0000.000
172A179GLU-1-0.941-0.96050.9790.0020.0020.0000.0000.0000.000
173A180VAL00.0010.00754.087-0.001-0.0010.0000.0000.0000.000
174A181LEU0-0.060-0.03848.519-0.001-0.0010.0000.0000.0000.000
175A182ARG10.8650.94851.9650.0000.0000.0000.0000.0000.000
176A183LYS10.8930.93154.2030.0000.0000.0000.0000.0000.000
177A184GLY0-0.0040.02256.7660.0000.0000.0000.0000.0000.000
178A185VAL00.007-0.02358.3580.0010.0010.0000.0000.0000.000
179A186GLU-1-0.978-0.97361.2030.0000.0000.0000.0000.0000.000
180A187PRO0-0.023-0.00363.9670.0000.0000.0000.0000.0000.000